A. Warshel

Most-cited papers

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis.
A. Warshel, R. Bora
2016Journal of Chemical Physics189 citations Open access
Semantic Scholar
The Physics and Physical Chemistry of Molecular Machines
R. Astumian, S. Mukherjee, A. Warshel
2016ChemPhysChem141 citations Open access
Semantic Scholar
Exploring the free-energy landscape of GPCR activation
R. Alhadeff, I. Vorobyov, H. Yoon, A. Warshel
2018Proceedings of the National Academy of Sciences of the United States of America58 citations Open access
Semantic Scholar
Harnessing generative AI to decode enzyme catalysis and evolution for enhanced engineering
Wen-Jun Xie, A. Warshel
2023bioRxiv56 citations Open access
Semantic Scholar
Critical Differences Between the Binding Features of the Spike Proteins of SARS-CoV-2 and SARS-CoV
Chen Bai, A. Warshel
2020Journal of Physical Chemistry B55 citations Open access
Semantic Scholar
Predicting Mutational Effects on Receptor Binding of the Spike Protein of SARS-CoV-2 Variants
Chen Bai, Junlin Wang, Geng Chen, Honghui Zhang +7 more
2021Journal of the American Chemical Society52 citations Open access
Semantic Scholar
Exploring the mechanism of covalent inhibition: Simulating the binding free energy of alpha-ketoamide inhibitors of the Main Protease of SAR-CoV-2
D. Mondal, A. Warshel
2020Biochemistry51 citations Open access
Semantic Scholar
Enhancing computational enzyme design by a maximum entropy strategy
Wen-Jun Xie, M. Asadi, A. Warshel
2022Proceedings of the National Academy of Sciences of the United States of America44 citations Open access
Semantic Scholar
Revisiting the protomotive vectorial motion of F0-ATPase
Chen Bai, A. Warshel
2019Proceedings of the National Academy of Sciences of the United States of America42 citations Open access
Semantic Scholar
Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase
Garima Jindal, K. Slánská, Veselin Kolev, J. Damborský +2 more
2018Proceedings of the National Academy of Sciences of the United States of America34 citations Open access
Semantic Scholar
Electrostatic influence on IL-1 transport through the GSDMD pore
Wen-Jun Xie, S. Xia, A. Warshel, Hao Wu
2022Proceedings of the National Academy of Sciences of the United States of America33 citations Open access
Semantic Scholar
Exploring the Catalytic Reaction of Cysteine Proteases.
G. Oanca, M. Asadi, A. Saha, Balajee Ramachandran +1 more
2020Journal of Physical Chemistry B33 citations
Semantic Scholar
ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion
Yarden Golan, R. Alhadeff, A. Warshel, Y. Assaraf
2019PLoS Comput. Biol.33 citations Open access
Semantic Scholar
Exploring the Catalytic Mechanism of Cas9 Using Information Inferred from Endonuclease VII
H. Yoon, Li-Na Zhao, A. Warshel
2018ACS Catalysis33 citations Open access
Semantic Scholar
On the control of the proton current in the voltage-gated proton channel Hv1
Myungjin Lee, Chen Bai, M. Feliks, R. Alhadeff +1 more
2018Proceedings of the National Academy of Sciences of the United States of America32 citations Open access
Semantic Scholar
Misunderstanding the Preorganization Concept can lead to Confusions about the Origin of Enzyme Catalysis
Garima Jindal, A. Warshel
2017Proteins: Structure, Function, and Bioinformatics32 citations Open access
Semantic Scholar
Exploring the Development of Ground-State Destabilization and Transition-State Stabilization in Two Directed Evolution Paths of Kemp Eliminases
Garima Jindal, Balajee Ramachandran, R. Bora, A. Warshel
2017ACS Catalysis31 citations Open access
Semantic Scholar
Simulating the dynamics of the mechanochemical cycle of myosin-V
S. Mukherjee, R. Alhadeff, A. Warshel
2017Proceedings of the National Academy of Sciences of the United States of America31 citations Open access
Semantic Scholar
The FOF1 ATP synthase: from atomistic three-dimensional structure to the rotary-chemical function
S. Mukherjee, A. Warshel
2017Photosynthesis Research30 citations Open access
Semantic Scholar
Simulating the Fidelity And The Three Mg Mechanism of Pol η and clarifying the validity of transition state theory in enzyme catalysis
H. Yoon, A. Warshel
2017Proteins: Structure, Function, and Bioinformatics30 citations Open access
Semantic Scholar
A Chemical Strategy for the Degradation of the Main Protease of SARS-CoV-2 in Cells.
Xiaohong Sang, Juan Wang, Jiao Zhou, Yan Xu +3 more
2023Journal of the American Chemical Society29 citations
Semantic Scholar
Exploring the Activation Process of the β2AR‑Gs Complex
Chen Bai, Junlin Wang, D. Mondal, Yang Du +2 more
2021Journal of the American Chemical Society26 citations Open access
Semantic Scholar
Reexamining the origin of the directionality of myosin V
R. Alhadeff, A. Warshel
2017Proceedings of the National Academy of Sciences of the United States of America25 citations Open access
Semantic Scholar
Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions
Jerônimo Lameira, Ilya Kupchencko, A. Warshel
2016Journal of Physical Chemistry B25 citations Open access
Semantic Scholar
Natural Evolution Provides Strong Hints about Laboratory Evolution of Designer Enzymes
Wen-Jun Xie, A. Warshel
2022Proceedings of the National Academy of Sciences of the United States of America24 citations Open access
Semantic Scholar
Origin of the Non-Arrhenius Behavior of the Rates of Enzymatic Reactions
Subhendu Roy, P. Schopf, A. Warshel
2017Journal of Physical Chemistry B24 citations Open access
Semantic Scholar
A new class of α-ketoamide derivatives with potent anticancer and anti-SARS-CoV-2 activities
Juan Wang, Boqiang Liang, Yiling Chen, Jasper Fuk-Woo Chan +13 more
2021European journal of medicinal chemistry23 citations Open access
Semantic Scholar
Combinatorial Approach for Exploring Conformational Space and Activation Barriers in Computer-Aided Enzyme Design
D. Mondal, V. Kolev, A. Warshel
2020ACS Catalysis23 citations Open access
Semantic Scholar
Exploring the Proteolysis Mechanism of the Proteasomes
A. Saha, G. Oanca, D. Mondal, A. Warshel
2020Journal of Physical Chemistry B23 citations Open access
Semantic Scholar
Exploring alternative catalytic mechanisms of Cas9 HNH domain
Li-Na Zhao, D. Mondal, A. Warshel
2019Proteins: Structure, Function, and Bioinformatics21 citations Open access
Semantic Scholar
The catalytic dwell in ATPases is not crucial for movement against applied torque
Chen Bai, M. Asadi, A. Warshel
2020Nature Chemistry20 citations
Semantic Scholar
EF-Tu and EF-G are activated by allosteric effects
D. Mondal, A. Warshel
2018Proceedings of the National Academy of Sciences of the United States of America20 citations Open access
Semantic Scholar
Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β
R. Matute, H. Yoon, A. Warshel
2016Proteins: Structure, Function, and Bioinformatics19 citations Open access
Semantic Scholar
Fast and Effective Prediction of the Absolute Binding Free Energies of Covalent Inhibitors of SARS-CoV-2 Main Protease and 20S Proteasome
Jiao Zhou, A. Saha, Ziwei Huang, A. Warshel
2022Journal of the American Chemical Society18 citations Open access
Semantic Scholar
A free-energy landscape for the glucagon-like peptide 1 receptor GLP1R
R. Alhadeff, A. Warshel
2019Proteins: Structure, Function, and Bioinformatics18 citations Open access
Semantic Scholar
Enhancing Luciferase Activity and Stability through Generative Modeling of Natural Enzyme Sequences
Wen-Jun Xie, Dangliang Liu, Xiaoya Wang, Aoxuan Zhang +4 more
2023bioRxiv17 citations Open access
Semantic Scholar
Validating a Coarse-Grained Voltage Activation Model by Comparing Its Performance to the Results of Monte Carlo Simulations
Myungjin Lee, V. Kolev, A. Warshel
2017Journal of Physical Chemistry B17 citations Open access
Semantic Scholar
Fine-tuning activation specificity of G-protein-coupled receptors via automated path searching
Ru-Juan Ti, Bin Pang, Lei-Ye Yu, Bing Gan +4 more
2024Proceedings of the National Academy of Sciences of the United States of America16 citations Open access
Semantic Scholar
Assessing the Catalytic Role of Native Glucagon Amyloid Fibrils
A. Nandi, Aoxuan Zhang, Elad Arad, R. Jelinek +1 more
2024ACS Catalysis16 citations Open access
Semantic Scholar
Analyzing the Reaction of Orotidine 5’-phosphate decarboxylase as a Way to Examine Some Key Catalytic Proposals
M. Asadi, A. Warshel
2022Journal of the American Chemical Society16 citations Open access
Semantic Scholar
Exploring the activation pathway and Gi-coupling specificity of the μ-opioid receptor
D. Mondal, V. Kolev, A. Warshel
2020Proceedings of the National Academy of Sciences of the United States of America16 citations Open access
Semantic Scholar
Theory and applications of the empirical valence bond approach : from physical chemistry to chemical biology
Fernanda Duarte, Shina Caroline Lynn Kamerlin, A. Warshel
201716 citations
Semantic Scholar
Exploring the Effectiveness of Binding Free Energy Calculations
D. Mondal, Jacob Florian, A. Warshel
2019Journal of Physical Chemistry B14 citations Open access
Semantic Scholar
Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter
Yarden Golan, R. Alhadeff, F. Glaser, Assaf Ganoth +2 more
2018PLoS Comput. Biol.13 citations Open access
Semantic Scholar
Biochemical and Computational Characterization of Haloalkane Dehalogenase Variants Designed by Generative AI: Accelerating the SN2 Step
N. Gelfand, V. Orel, Wenqiang Cui, J. Damborský +4 more
2025Journal of the American Chemical Society12 citations Open access
Semantic Scholar
MEDIATE - Molecular DockIng at homE: Turning collaborative simulations into therapeutic solutions
G. Vistoli, C. Manelfi, C. Talarico, A. Fava +20 more
2023Expert Opinion on Drug Discovery12 citations Open access
Semantic Scholar
Energetic and Structural Insights behind Calcium induced Conformational Transition in Calmodulin
Ritaban Halder, A. Warshel
2023Proteins: Structure, Function, and Bioinformatics12 citations Open access
Semantic Scholar
Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations
H. Yoon, V. Kolev, A. Warshel
2017Journal of Physical Chemistry B11 citations Open access
Semantic Scholar
Exploring the role of chemical reactions in the selectivity of tyrosine kinase inhibitors
M. Asadi, Wen-Jun Xie, A. Warshel
2022Journal of the American Chemical Society10 citations Open access
Semantic Scholar
Exploring the Drug Resistance of HCV Protease
Garima Jindal, D. Mondal, A. Warshel
2017Journal of Physical Chemistry B10 citations Open access
Semantic Scholar